Document Type
Journal Article
Publication Date
6-2016
Journal
Open Forum Infectious Diseases
Volume
3
Issue
3
DOI
10.1093/ofid/ofw129
Abstract
Background. Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence type 131 (ST131) has been inferred based on conventional typing data, but has been assessed minimally using whole genome sequence (WGS) analysis.
Methods. Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in six households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates.
Results. In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed between H30R1 and H30Rx comparison genomes. For only one household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these two groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In one instance the household's index strain persisted for 6 years before causing a new infection in a different household member.
Conclusions. Within-household sharing of E. coli ST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members.
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
APA Citation
Johnson, J. R., Davis, G., Clabots, C., Johnston, B. D., Porter, S., Price, L. B., & +10 additional authors (2016). Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis. Open Forum Infectious Diseases, 3 (3). http://dx.doi.org/10.1093/ofid/ofw129
Peer Reviewed
1
Open Access
1
Included in
Bacteriology Commons, Environmental Public Health Commons, Occupational Health and Industrial Hygiene Commons
Comments
Reproduced with permission of Oxford University Press. Open Forum Infectious Diseases.